1
|
Liu Q, Cai Y, Xiong H, Deng Y, Dai X. CCRDB: a cancer circRNAs-related database and its application in hepatocellular carcinoma-related circRNAs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5520605. [PMID: 31219565 PMCID: PMC6585150 DOI: 10.1093/database/baz063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/30/2019] [Accepted: 04/09/2019] [Indexed: 01/28/2023]
Abstract
Circular RNAs (circRNAs) are widely expressed in human cells and tissues and can form a covalently closed exon circularization, which have stable patterns and play important regulatory roles in physiological or pathological process. There is still lack of a comprehensively disease-related knowledge base for in-depth analysis of circRNAs. In this paper, a cancer circRNAs-related database (CCRDB) was established. The CCRDB’s initial circRNAs data were collected by sequencing experimental data of 10 samples from 5 patients with hepatocellular carcinoma (HCC), where a total of 11 501 circRNAs were found and can easily be expanded by collecting and analyzing external data sources such as circBASE (1). Using CCRDB, we have further studied the relationships between circRNAs and HCC and found that circRNAs (hsa_circ_ 0002130, hsa_circ_0084615, hsa_circ_0001445, hsa_circ_0001727 and hsa_circ_0001361) and the corresponding genes ID [C3 (2, 3), ASPH (4), SMARCA5 (5), ZKSCAN1 (6) and FNDC3B (7)], respectively, might be the potential biomarker targets for HCC. Furthermore, our experiment also found that some new circRNAs chromosome sites chr12:23998917 24048958 and chr16:72090429 72093087 and the corresponding genes ID (SOX5 (8) and HP (9), respectively), might be the potential biomarker targets for HCC. These results indicate that CCRDB can effectively reveal the relationships between circRNAs and HCC. As the first circRNAs database to provide analysis and comparison functions, it is of great significance for researchers to further study the rules of circRNAs, to understand the causes of circRNAs in disease discovery and to find target genes for therapeutic approaches.
Collapse
Affiliation(s)
- Qingyu Liu
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yanning Cai
- Jinan University, No. 601, West Huangpu Avenue, Guangzhou, Guangdong, China
| | - Haiquan Xiong
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yiyun Deng
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| |
Collapse
|
2
|
Zayet S, Osman M, Besghaier H, Ben Moussa M, Belhadj A, Bellaaj R. [Prevalence of hepatitis B markers and vaccination status of healthcare personnel: Experience of the Tunis Military Hospital]. Rev Epidemiol Sante Publique 2019; 67:261-266. [PMID: 31060884 DOI: 10.1016/j.respe.2019.03.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 02/14/2019] [Accepted: 03/04/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hepatitis B is the main cause of liver disease in the world. Chronic hepatitis B may lead to cirrhosis, liver insufficiency or liver cancer. Tunisia is considered as a country with intermediate endemicity, where hepatitis B presents a real public health problem. The aims of this study were to evaluate the prevalence of viral biomarkers of hepatitis B in healthcare personnel; to look for potential risk factors associated with HbS antigen carriage and to evaluate the prevalence of vaccination in this particular population. METHODS Sero-epidemiological, prospective and descriptive study, among 2411 healthcare personnel in the Military Hospital of Tunis, during a 5-month period from September 2013 to January 2014. RESULTS Blood samples were collected from 1497 volunteers among the hospital staff. Two hundred and seventy-one individuals had a positive HbC antibody titer (prevalence 18.1%), including 229 who were positive for HbC and HbS antibodies (prevalence 15.3%), 12 positive for only HbC antibody (prevalence 0.8%), and 30 positive for HBsAg (prevalence 2%). Among HbS Ag carriers, 56.6% reported needle stick and sharp object injuries during their professional careers. Among HbS Ag carriers, there were three patients with a history of acute viral hepatitis with jaundice, and 27 patients (90%) who were asymptomatic and were diagnosed during our study. Among healthcare workers in the hospital, 56.1% were immunized through vaccination (positive HbS antibodies without HbC antibodies), of whom 66% had durable protective immunity (HbS antibodies>100mU/mL). Lastly, 25.8% of the hospital workers remained without any protection against hepatitis B (serology entirely negative) and were then offered a complete vaccination. CONCLUSION Hepatitis B vaccine is the mainstay of hepatitis B prevention. Safe injection practices, blood safety and promoting wider access to monitoring and screening, care and treatment services for hepatitis B are the best guarantees to prevent and control this disease.
Collapse
Affiliation(s)
- S Zayet
- Service des maladies infectieuses, hôpital La Rabta, Tunis, Tunisie.
| | - M Osman
- Service d'hygiène hospitalière et de protection de l'environnement, hôpital militaire principal et d'instruction de Tunis, Tunis, Tunisie
| | - H Besghaier
- Service de médecine du travail et de sécurité professionnelle, hôpital militaire principal et d'instruction de Tunis, Tunis, Tunisie
| | - M Ben Moussa
- Laboratoire de microbiologie, hôpital militaire principal et d'instruction de Tunis, Tunis, Tunisie
| | - A Belhadj
- Service de médecine du travail et de sécurité professionnelle, hôpital militaire principal et d'instruction de Tunis, Tunis, Tunisie
| | - R Bellaaj
- Service d'hygiène hospitalière et de protection de l'environnement, hôpital militaire principal et d'instruction de Tunis, Tunis, Tunisie
| |
Collapse
|
3
|
Circular RNAs as novel biomarkers with regulatory potency in human diseases. Future Sci OA 2018; 4:FSO314. [PMID: 30112184 PMCID: PMC6088266 DOI: 10.4155/fsoa-2018-0036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs characterized with closed loop structures without 3′ and 5′ polar ends. They can roughly be divided into exonic circRNAs, exon–intron circRNAs and circular intronic RNAs. CircRNAs are characterized with stability, prevalence, specificity and conservation, which arouse great interest in circRNAs as disease biomarkers. Their abilities to sponge to miRNAs, cis-regulate parent genes, bind to proteins and encode proteins endow circRNAs a critical role of regulation in eukaryotic cells. This concise review focuses on circRNAs as functional biomarkers and therapeutic targets in both tumor and nontumorous diseases. Although they were discovered in 1970s, circular RNAs (circRNAs) have attracted great interest only relatively recently. Instead of genome ‘junk matters’, circRNAs are now considered as promising biomarkers and treatment targets. CircRNAs are involved in numerous cancer-related and noncancer diseases, such as lung cancer, gastric cancer, cardiovascular diseases, diabetes mellitus and so on. This review outlines the classification, characterization and function of circRNAs, with a specific focus on recent studies concerning the role of circRNAs in human diseases.
Collapse
|
4
|
Boa A, Douba A, N Guessan TB, Menan H, Attia A, Ouassa T, Bénié JBV, Abokon A, Dosso M, Aholi P, Timité-Konan M, Abauleth RY, Bissagnéné E, Aka J, Yavo JC, Sylvain BJ, Ouattara GS, Ekra DK, Sow K, Kouassi JNG, Ahoussou EMK, Dally RK. [A plea for introduction of hepatitis B vaccination at birth in Côte d'Ivoire]. SANTE PUBLIQUE (VANDOEUVRE-LES-NANCY, FRANCE) 2017; 29:751-760. [PMID: 29384309 DOI: 10.3917/spub.175.0751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The Côte d'Ivoire National Immunization Technical Advisory Group 2015 work plan included elaboration of an opinion on inclusion of hepatitis B vaccination at birth in the Expanded Program on Immunization (EPI) in Côte d'Ivoire. A task force was set up to conduct this assessment according to a systematized method. The task force analysed scientific articles on the burden of hepatitis B in Côte d'Ivoire, the burden of mother-child transmission, the impact of hepatitis B vaccination at birth in countries which have adopted this strategy, the efficacy and safety of hepatitis B vaccine in newborns, the cost-effectiveness of hepatitis B vaccination at birth, and the best strategy to introduce hepatitis B vaccination at birth in the EPI. The National Immunization Technical Advisory Group of Côte d'Ivoire finally recommended introduction of a dose of hepatitis B vaccine at birth in the context of the Expanded Program on Immunization with maintenance of three doses of pentavalent vaccine (DPT-HepB-Hib) at 6, 10, and 14 weeks of age.
Collapse
|
5
|
Li Y, Dong Y, Huang Z, Kuang Q, Wu Y, Li Y, Li M. Computational identifying and characterizing circular RNAs and their associated genes in hepatocellular carcinoma. PLoS One 2017; 12:e0174436. [PMID: 28346469 PMCID: PMC5367815 DOI: 10.1371/journal.pone.0174436] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/09/2017] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT. We found significant candidate circRNAs expression alterations between normal and tumor samples. Additionally, the PCGs associated with these candidate circRNAs were also found have discriminative expression patterns between normal and tumor samples. The enrichment analysis illustrated that these PCGs were predominantly enriched for liver/cardiovascular-related diseases such as atherosclerosis, myocardial ischemia and coronary heart disease, and participated in various metabolic processes. Together, a further network analysis indicated that these PCGs play important roles in the regulatory and the PPI network. Finally, we built a classification model to distinguish normal and tumor samples by using candidate circRNAs and their associated genes, respectively. Both of them obtained satisfactory results (~ 0.99 of AUC for circRNA and PCG). Our findings suggested that the circRNA could be a critical factor in HCC, providing a useful resource to explore the pathogenesis of HCC.
Collapse
Affiliation(s)
- Yan Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yongcheng Dong
- College of Life Science, Sichuan University, Chengdu, China
| | - Ziyan Huang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Qifan Kuang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yiming Wu
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, China
- * E-mail: (ML); (YiL)
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
- * E-mail: (ML); (YiL)
| |
Collapse
|
6
|
El Saghir NS, Farhat RA, Charara RN, Khoury KE. Enhancing cancer care in areas of limited resources: our next steps. Future Oncol 2015; 10:1953-65. [PMID: 25386812 DOI: 10.2217/fon.14.124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In-depth knowledge of local conditions is necessary in order to enhance care in low- and middle-income countries. In this review we discuss: improving cancer diagnosis, optimizing patient management, increasing health awareness, prevention, early detection, eradication of causative infectious diseases and agents, tobacco control, healthy diets and lifestyles, availability of diagnostic methods, easy access to care, affordable costs, improving infrastructures, quality care measures, implementing and adapting guidelines, multidisciplinary management, supportive and survivorship care, research and optimization of medical school curriculum and training in oncology. Establishment of national cancer control plans by policy makers, physician societies, medical schools, and patient advocates is recommended. We will review evidence and controversies, and outline the next steps needed to prevent cancer and enhance care of cancer patients in LMICs.
Collapse
Affiliation(s)
- Nagi S El Saghir
- Breast Center of Excellence, Naef K. Basile Cancer Institute, Division of Hematology Oncology, Department of Internal Medicine, American University of Beirut Medical Center, PO Box 11-0236, Riad El Solh 1107 2020, Beirut, Lebanon
| | | | | | | |
Collapse
|
7
|
Delany I, Rappuoli R, De Gregorio E. Vaccines for the 21st century. EMBO Mol Med 2014; 6:708-20. [PMID: 24803000 PMCID: PMC4203350 DOI: 10.1002/emmm.201403876] [Citation(s) in RCA: 274] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/20/2014] [Accepted: 04/07/2014] [Indexed: 12/18/2022] Open
Abstract
In the last century, vaccination has been the most effective medical intervention to reduce death and morbidity caused by infectious diseases. It is believed that vaccines save at least 2-3 million lives per year worldwide. Smallpox has been eradicated and polio has almost disappeared worldwide through global vaccine campaigns. Most of the viral and bacterial infections that traditionally affected children have been drastically reduced thanks to national immunization programs in developed countries. However, many diseases are not yet preventable by vaccination, and vaccines have not been fully exploited for target populations such as elderly and pregnant women. This review focuses on the state of the art of recent clinical trials of vaccines for major unmet medical needs such as HIV, malaria, TB, and cancer. In addition, we describe the innovative technologies currently used in vaccine research and development including adjuvants, vectors, nucleic acid vaccines, and structure-based antigen design. The hope is that thanks to these technologies, more diseases will be addressed in the 21st century by novel preventative and therapeutic vaccines.
Collapse
|
8
|
Tanase AM, Dumitrascu T, Dima S, Grigorie R, Marchio A, Pineau P, Popescu I. Influence of hepatitis viruses on clinicopathological profiles and long-term outcome in patients undergoing surgery for hepatocellular carcinoma. Hepatobiliary Pancreat Dis Int 2014; 13:162-72. [PMID: 24686543 DOI: 10.1016/s1499-3872(14)60026-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The global risk of hepatocellular carcinoma (HCC) is largely due to hepatitis B virus (HBV) and hepatitis C virus (HCV) infections. In recent years, however, an increased prevalence of non-viral HCC has been noted. The clinical impact of the presence/absence of viral infections in HCC remains controversial. The present study aimed to assess the effect of hepatitis viruses on demographics, clinical and pathological features and long-term outcome in a large cohort of Romanian patients who underwent surgery for HCC. METHODS The study included 404 patients with HCC who had undergone resection, transplantation or radiofrequency ablation at a single institution between 2001 and 2010. The patients were divided into four groups: 85 patients with hepatitis B virus infection (HBV group), 164 patients with hepatitis C virus infection (HCV group), 39 patients with hepatitis B and C virus co-infection (HBCV group), and 116 patients without viral infection (non-BC group). RESULTS The patients of both HBV (56.0+/-11.3 years) and HBCV groups (56.0+/-9.9 years) were significantly younger than those of the HCV (61.0+/-8.5 years, P=0.001) and non-BC groups (61.0+/-13.0 years, P=0.002). Interestingly, the prevalence of liver cirrhosis was significantly lower in the non-BC group (47%) than in any other subsets (72%-90%, P<0.002). Furthermore, the non-BC patients were more advanced according to the Barcelona Clinic Liver Cancer stages than the patients of the HCV or HBCV groups (P<0.020); accordingly, they were more frequently assessed beyond the Milan criteria than any other groups (P=0.001). No significant differences in the disease-free or overall survival rates were observed among these groups. CONCLUSIONS Patients with non-viral HCC are diagnosed at advanced ages and stages, a situation plausibly due to the poor effectiveness of cancer surveillance in community practice. The presence of viral infections does not appear to impair the long-term prognosis after surgical treatment in patients with HCC; however, there is a trend for worse disease-free survival rates in HBCV patients, though statistical significance was not reached.
Collapse
Affiliation(s)
- Anna-Maria Tanase
- Center of General Surgery and Liver Transplant, Fundeni Clinical Institute, Fundeni Street No. 258, 022328, Bucharest, Romania.
| | | | | | | | | | | | | |
Collapse
|
9
|
Huang Q, Tan Y, Yin P, Ye G, Gao P, Lu X, Wang H, Xu G. Metabolic characterization of hepatocellular carcinoma using nontargeted tissue metabolomics. Cancer Res 2013; 73:4992-5002. [PMID: 23824744 DOI: 10.1158/0008-5472.can-13-0308] [Citation(s) in RCA: 308] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hepatocellular carcinoma has a poor prognosis due to its rapid development and early metastasis. In this report, we characterized the metabolic features of hepatocellular carcinoma using a nontargeted metabolic profiling strategy based on liquid chromatography-mass spectrometry. Fifty pairs of liver cancer samples and matched normal tissues were collected from patients having hepatocellular carcinoma, including tumor tissues, adjacent noncancerous tissues, and distal noncancerous tissues, and 105 metabolites were filtered and identified from the tissue metabolome. The principal metabolic alternations in HCC tumors included elevated glycolysis, gluconeogenesis, and β-oxidation with reduced tricarboxylic acid cycle and Δ-12 desaturase. Furthermore, increased levels of glutathione and other antioxidative molecules, together with decreased levels of inflammatory-related polyunsaturated fatty acids and phospholipase A2, were observed. Differential metabolite levels in tissues were tested in 298 serum specimens from patients with chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Betaine and propionylcarnitine were confirmed to confer good diagnostic potential to distinguish hepatocellular carcinoma from chronic hepatitis and cirrhosis. External validation of cirrhosis and hepatocellular carcinoma serum specimens further showed that this combination biomarker is useful for diagnosis of hepatocellular carcinoma with a supplementary role to α-fetoprotein.
Collapse
Affiliation(s)
- Qiang Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Rappuoli R, Mandl CW, Black S, De Gregorio E. Vaccines for the twenty-first century society. Nat Rev Immunol 2011; 11:865-72. [PMID: 22051890 PMCID: PMC7098427 DOI: 10.1038/nri3085] [Citation(s) in RCA: 276] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The childhood vaccination campaigns of the twentieth century represent one of the great success stories of modern medicine. But are we yet to realize the full potential of vaccines? This article discusses the medical needs of the twenty-first century society and proposes that new vaccines will play a major part in addressing these needs. Vaccines have been one of the major revolutions in the history of mankind and, during the twentieth century, they eliminated most of the childhood diseases that used to cause millions of deaths. In the twenty-first century, vaccines will also play a major part in safeguarding people's health. Supported by the innovations derived from new technologies, vaccines will address the new needs of a twenty-first century society characterized by increased life expectancy, emerging infections and poverty in low-income countries.
Collapse
Affiliation(s)
- Rino Rappuoli
- Novartis Vaccines & Diagnostics Srl, Via Fiorentina 5, 53100 Siena, Italy.
| | | | | | | |
Collapse
|